Contacts of the helix formed by residues 205 - 221 (chain B) in PDB entry 3E7O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 4.3 1.4 - - - +
203B LYS* 3.1 13.4 + - - +
204B GLU* 1.3 75.2 - - + +
206B VAL* 1.3 65.2 + - - +
207B ASP 3.1 1.1 - - - +
208B ILE* 3.3 18.9 + - + +
209B TRP 3.6 0.2 + - - -
306B PRO* 2.8 38.2 + - - +
309B ARG* 3.0 49.9 + - - +
310B ILE 3.7 17.9 + - - +
311B SER* 4.6 7.7 - - - +
312B VAL* 5.5 0.9 - - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE* 3.6 22.7 - - + -
150B ARG* 3.9 13.0 - - + -
193B ALA* 3.6 23.7 - - + +
195B GLU* 3.8 12.8 + - - +
196B VAL* 3.8 20.9 - - + -
202B TYR* 3.7 20.0 - - + -
203B LYS 3.0 18.7 + - - +
204B GLU 2.9 0.8 + - - -
205B ASN* 1.3 79.4 + - - +
207B ASP* 1.3 70.6 + - - +
209B TRP* 3.4 18.2 + - - +
210B SER* 3.7 8.2 + - - -
309B ARG* 3.9 1.1 - - - +
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Residues in contact with ASP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ILE* 4.2 12.7 - - + +
143B HIS* 3.0 26.7 + - + +
148B ILE* 3.8 1.4 - - - +
149B HIS* 3.0 27.2 + - - +
150B ARG* 2.8 31.9 + - - -
152B LEU* 3.9 15.9 - - + +
204B GLU 3.2 8.2 + - - +
205B ASN 3.1 0.4 - - - -
206B VAL* 1.3 80.0 - - - +
208B ILE* 1.3 58.1 + - - +
210B SER* 3.4 9.8 + - - -
211B VAL* 3.1 31.3 + - - +
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.7 29.6 - - + -
139B ILE* 6.4 0.2 - - + -
205B ASN* 3.3 16.7 + - - +
207B ASP* 1.3 75.5 - - - +
209B TRP* 1.3 66.5 + - - +
211B VAL* 3.2 5.1 + - + +
212B GLY* 2.8 21.3 + - - -
301B MET* 3.7 27.0 - - + +
309B ARG* 3.8 11.4 - - + -
310B ILE* 3.5 27.6 - - + +
311B SER 3.9 5.4 - - - +
312B VAL* 3.9 34.5 - - + +
315B ALA* 4.1 7.2 - - + -
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Residues in contact with TRP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR 5.0 1.2 + - - -
191B TYR 3.5 12.2 - - - -
192B ARG 3.4 11.9 + - - -
193B ALA* 3.4 28.3 - - + -
194B PRO* 3.4 32.5 - - + -
205B ASN 3.6 3.2 + - - -
206B VAL 3.4 12.0 + - - +
207B ASP 3.4 0.2 - - - -
208B ILE* 1.3 78.0 - - - +
210B SER* 1.3 57.0 + - - +
212B GLY* 3.1 4.0 + - - -
213B CYS* 2.9 40.9 + - - -
225B PHE* 3.5 25.5 - + - -
237B VAL* 3.9 15.0 - - + -
241B LEU* 3.7 20.4 - - + -
301B MET 4.0 13.2 - - - -
302B LEU* 3.8 9.4 - - + +
303B VAL 3.6 38.8 - - - -
304B ILE* 4.0 1.1 - - + -
309B ARG* 3.9 9.3 - - - +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ARG* 5.1 5.5 + - - -
152B LEU* 3.8 37.2 + - - +
191B TYR* 3.0 24.6 + - - -
193B ALA 5.2 0.7 + - - -
206B VAL 3.7 9.9 + - - -
207B ASP* 3.4 13.2 + - - -
208B ILE 3.3 0.2 - - - -
209B TRP* 1.3 76.5 - - - +
211B VAL* 1.3 58.3 + - - +
213B CYS* 3.1 5.5 + - - +
214B ILE* 2.9 35.9 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 4.1 20.5 - - + +
135B MET* 4.6 13.7 - - + -
136B LEU* 4.3 16.4 - - + -
139B ILE* 3.4 29.6 - - + -
152B LEU* 4.7 3.6 - - + -
207B ASP 3.1 16.9 + - - +
208B ILE* 3.6 9.6 - - - +
210B SER* 1.3 74.3 - - - +
212B GLY* 1.3 52.6 + - - +
214B ILE* 3.3 8.7 + - + +
215B MET* 2.8 34.0 + - - +
301B MET* 4.0 22.7 - - + -
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Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE 2.8 14.0 + - - -
209B TRP 3.1 4.7 + - - -
211B VAL* 1.3 77.0 - - - +
213B CYS* 1.3 56.1 + - - +
215B MET* 4.3 3.1 - - - -
216B GLY* 2.9 25.3 + - - -
298B LEU* 3.5 11.4 - - - +
301B MET* 3.9 20.3 - - - -
302B LEU* 3.6 18.8 - - - +
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Residues in contact with CYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR 4.0 10.8 - - - +
191B TYR* 3.6 22.3 - - + -
209B TRP* 2.9 45.1 + - - +
210B SER* 3.1 8.5 + - - +
212B GLY* 1.3 72.8 - - - +
214B ILE* 1.3 60.9 + - - +
216B GLY 3.6 0.2 + - - -
217B GLU* 3.1 29.8 + - - +
224B ILE* 3.8 13.6 + - + +
225B PHE* 3.8 25.6 - - - -
302B LEU* 4.0 2.0 - - - -
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.6 29.8 - - + -
119B ILE* 5.5 2.1 - - + +
135B MET* 4.0 17.0 - - + -
152B LEU* 4.2 8.5 - - + +
153B LYS* 4.0 23.8 - - - +
154B PRO* 4.0 22.7 - - + -
157B ILE* 4.1 16.2 - - + -
191B TYR* 4.3 7.0 - - + -
210B SER 2.9 25.9 + - - +
211B VAL* 3.7 7.6 - - + +
213B CYS* 1.3 73.8 - - - +
215B MET* 1.3 59.7 + - - +
217B GLU* 3.2 7.5 + - - +
218B LEU* 2.9 34.6 + - + +
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Residues in contact with MET 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.7 44.6 - - + +
211B VAL 2.8 21.6 + - - +
212B GLY* 3.7 5.2 - - - +
214B ILE* 1.3 72.9 - - - +
216B GLY* 1.3 63.6 + - - +
218B LEU* 3.3 8.4 + - - +
219B VAL* 3.2 29.8 + - + +
294B ALA* 3.2 45.3 - - + +
297B LEU* 3.9 25.4 - - + -
298B LEU* 3.8 20.9 - - + -
301B MET* 4.6 6.3 - - - +
320B TYR* 4.1 4.0 - - + -
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLY 2.9 17.5 + - - -
215B MET* 1.3 74.5 - - - +
217B GLU* 1.3 51.2 + - - +
219B VAL* 3.4 3.9 + - - +
220B LYS* 2.8 37.9 + - - +
224B ILE* 3.5 14.1 - - - +
275B PHE* 3.7 21.7 - - - -
298B LEU* 3.6 7.9 - - - +
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Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 3.4 38.2 - - + +
154B PRO* 4.1 2.1 - - - +
191B TYR* 2.5 40.6 + - - -
213B CYS 3.1 14.5 + - - +
214B ILE* 3.6 5.4 - - - +
216B GLY* 1.3 73.7 - - - +
218B LEU* 1.3 59.2 + - - +
221B GLY* 2.7 31.9 + - - -
222B SER* 3.3 27.7 - - - +
223B VAL* 3.7 23.6 + - - +
224B ILE* 3.8 1.6 + - + +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.6 5.2 - - + -
118B VAL* 3.5 34.8 - - + +
119B ILE* 4.1 28.9 - - + +
121B MET 5.0 5.0 - - - +
123B LEU* 4.7 6.2 - - + +
128B MET* 4.4 19.8 - - + +
131B LEU* 4.6 16.4 - - + -
132B LEU* 4.8 9.2 - - + -
135B MET* 4.3 14.6 - - + -
214B ILE* 2.9 31.9 + - + +
215B MET* 3.6 15.0 - - + +
217B GLU* 1.3 77.2 - - - +
219B VAL* 1.3 61.2 + - - +
221B GLY 4.3 2.1 + - - -
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 3.9 22.7 - - + -
215B MET* 3.2 26.1 + - + +
216B GLY* 3.6 8.5 - - - +
218B LEU* 1.3 78.7 - - + +
220B LYS* 1.3 60.6 + - - +
275B PHE* 4.4 4.5 - - + -
279B ILE* 3.5 46.6 - - + +
280B PHE* 3.6 39.3 - - + -
294B ALA* 5.8 0.2 - - + -
298B LEU* 5.0 2.9 - - + -
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLY 2.8 21.4 + - - +
219B VAL* 1.3 74.9 - - - +
221B GLY* 1.3 58.8 + - - +
222B SER* 3.2 27.8 + - - +
224B ILE* 4.1 8.3 - - + +
240B GLN* 5.3 6.8 + - - -
274B LEU* 3.2 29.3 + - - +
275B PHE* 3.9 13.0 - - + -
276B PRO* 5.3 1.3 - - - -
279B ILE* 3.8 27.2 - - + +
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Residues in contact with GLY 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 4.0 28.4 - - - +
120B HIS* 5.3 5.4 - - - -
217B GLU 2.7 19.5 + - - -
218B LEU 4.3 1.5 + - - -
219B VAL 3.6 1.4 - - - -
220B LYS* 1.3 72.4 - - - +
222B SER* 1.3 59.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il